Graphite carbon nitride (g-C₃N₄) is a common photocatalyst, but it only shows limited photocatalytic performance due to its inherent carrier recombination. Hence, a novel 1D/2D FeV₃O₈ nanorod/g-C₃N₄ nanosheet composite photocatalyst was synthesized. X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) confirmed that FeV₃O₈ and g-C₃N₄ were successfully coupled together and formed a clear and intimate interface. The optimized sample (FCN-10) exhibits superior performance for ibuprofen (IBF) degradation under visible light irradiation, and its kinetic rate constant is 4 times that of g-C₃N₄ nanosheets. Based on the band energy structure, reaction oxide species (ROS) quenching experiments and single-particle photoluminescence data analysis, we considered that a Z-scheme heterojunction was generated in the FCN system. For the first time, the Fukui index (f⁻), the highest occupied molecular orbital (HOMO), and atoms-in-molecules (AIM) topological analysis were used to analyze the active sites and covalent bonds of IBF molecules that were susceptible to the attack of ROS during photocatalysis, and the results were in good agreement with the LC-MS/MS intermediate detection. In addition, the toxicity of the transformation products was evaluated by quantitative structure–activity relationship (QSAR) analysis, suggesting that the proposed photocatalytic technique was a green method.